I just purchased the new i pod touch 5 th generation and it does not
fit in the port on my new beatbox dock.
The connection on the new i pod is much much smaller , none of
the dock adapters even come close to allowing me to fit the i pod into
the beatbox.

I have a few micro USB charging cables that are longer or shorter than standard Apple cables. Can I use those with the lightning to micro USB adapter, and still have no fear of overcharging my iphone 6S?

Hi!
First off good question, unfortunately there is no way to pull information from a USB to any iOS device.
I'd suggest using an app such as DropBox to keep files you need stored across all of your devices.